Low (dc) resistance isn't the issue: you can actually short your avr's pins without damaging them.
You've done this?
I guess Atmel doesn't know what they're talking about when they give the current limits, both per-output and per-device, in the datasheet.
The simple fact is, you kill the arduino (actually the ATmega) by trying to draw more current than the chip is designed to handle.
-j